Journal Article

Rational design of a helical peptide inhibitor targeting c-Myb–KIX interaction

Suetaka, Shunji, Arai, Munehito, Oka, Yoshiki, Hayashi, Yuuki, Kunihara, Tomoko

2022

Overview

The transcription factor c-Myb promotes the proliferation of hematopoietic cells by interacting with the KIX domain of CREB-binding protein; however, its aberrant expression causes leukemia. Therefore, inhibitors of the c-Myb–KIX interaction are potentially useful as antitumor drugs. Since the intrinsically disordered transactivation domain (TAD) of c-Myb binds KIX via a conformational selection mechanism where helix formation precedes binding, stabilizing the helical structure of c-Myb TAD is expected to increase the KIX-binding affinity. Here, to develop an inhibitor of the c-Myb–KIX interaction, we designed mutants of the c-Myb TAD peptide fragment where the helical structure is stabilized, based on theoretical predictions using AGADIR. Three of the four initially designed peptides each had a different Lys-to-Arg substitution on the helix surface opposite the KIX-binding interface. Furthermore, the triple mutant with three Lys-to-Arg substitutions, named RRR, showed a high helical propensity and achieved three-fold higher affinity to KIX than the wild-type TAD with a dissociation constant of 80 nM. Moreover, the RRR inhibitor efficiently competed out the c-Myb–KIX interaction. These results suggest that stabilizing the helical structure based on theoretical predictions, especially by conservative Lys-to-Arg substitutions, is a simple and useful strategy for designing helical peptide inhibitors of protein–protein interactions.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/114/469 / 631/45/470 / 631/57/2269 / 631/61/338/469 / Affinity / Binding Sites / c-Myb protein / Cell proliferation / CREB-binding protein / CREB-Binding Protein - chemistry / CREB-Binding Protein - metabolism / Cyclic AMP response element-binding protein / Drug Design / Humanities and Social Sciences / Leukemia / Models, Molecular / multidisciplinary / Mutant Proteins - chemistry / Mutant Proteins - metabolism / Mutants / Peptide inhibitors / Peptides / Peptides - chemistry / Peptides - metabolism / Peptides - pharmacology / Protein Binding / Protein Conformation / Protein Domains / Protein interaction / Protein Structure, Secondary / Proteins / Proto-Oncogene Proteins c-myb - genetics / Proto-Oncogene Proteins c-myb - metabolism / Science / Science (multidisciplinary)